Contacts of the helix formed by residues 231 - 240 (chain A) in PDB entry 2FBW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213A THR* 5.4 1.5 + - - -
214A GLY 4.9 3.4 - - - -
215A GLY 3.0 20.0 + - - -
216A TYR* 3.6 14.3 - - - +
230A THR* 1.3 77.2 - - - +
232A ASP* 1.3 64.9 + - - +
233A GLY 3.3 2.7 - - - -
234A THR* 3.3 13.2 + - - -
235A ALA* 3.1 22.5 + - - +
527A ASN* 4.4 0.2 - - - -
531A CYS* 3.8 8.2 - - - -
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Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LYS* 2.9 28.9 + - - +
177A PHE* 3.5 18.9 - - + -
178A ALA* 5.0 8.3 - - + +
213A THR* 5.0 13.2 + - + +
230A THR* 2.8 25.0 + - - +
231A GLY* 1.3 76.4 - - - +
233A GLY* 1.3 56.9 + - - +
235A ALA* 3.4 3.3 + - - +
236A MET* 3.1 33.1 + - + +
524A GLU* 4.0 2.3 - - - +
527A ASN* 2.8 32.2 + - - +
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Residues in contact with GLY 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A ILE* 3.8 11.5 - - - +
213A THR* 3.0 28.9 + - - +
231A GLY 3.3 0.2 - - - -
232A ASP* 1.3 76.1 - - - +
234A THR* 1.3 65.8 + - - +
236A MET* 3.3 14.8 + - - +
237A VAL* 3.2 26.0 + - - +
370A ILE* 4.0 6.4 - - - +
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 4.3 1.4 + - - -
214A GLY 4.6 8.3 + - - -
216A TYR* 4.6 7.6 - - + -
231A GLY* 3.6 14.3 + - - -
233A GLY* 1.3 76.0 - - - +
235A ALA* 1.3 57.6 + - - +
237A VAL* 3.4 4.2 + - - +
238A THR* 3.0 30.4 + - - +
244A CYS* 3.3 29.5 - - + -
247A LEU* 4.4 15.7 - - + -
369A GLY* 4.9 8.5 - - - -
370A ILE* 4.3 10.0 - - - +
398A ALA* 4.4 12.3 + - - +
531A CYS* 3.8 19.7 - - - -
534A GLN* 5.3 1.1 - - - +
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Residues in contact with ALA 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLY 3.1 9.2 + - - +
232A ASP 3.8 0.9 - - - +
234A THR* 1.3 74.6 - - - +
236A MET* 1.3 58.8 + - - +
238A THR* 3.3 7.7 + - - -
239A ARG* 2.8 41.2 + - - +
527A ASN* 3.4 52.5 - - + +
530A LEU* 4.1 8.5 - - + +
531A CYS* 4.6 1.5 - - - -
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Residues in contact with MET 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A VAL* 4.4 10.3 - - + -
178A ALA* 3.9 28.5 - - + +
179A LEU 3.8 17.3 - - - +
180A ASP* 3.5 37.6 - - - +
181A LEU* 4.2 20.2 + - + +
191A VAL* 5.4 1.1 - - + -
211A ILE* 3.8 28.5 - - + -
213A THR* 4.9 0.7 - - + -
232A ASP 3.1 14.2 + - - +
233A GLY* 3.3 18.8 + - - +
235A ALA* 1.3 75.5 - - - +
237A VAL* 1.3 61.9 + - + +
239A ARG* 3.3 10.7 + - - +
240A ALA* 3.0 22.3 + - - +
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Residues in contact with VAL 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 4.6 14.8 - - + -
211A ILE* 5.0 6.1 - - + -
233A GLY 3.2 12.3 + - - +
234A THR 3.6 7.2 - - - +
235A ALA 3.3 0.2 - - - -
236A MET* 1.3 76.4 - - + +
238A THR* 1.3 64.3 + - - +
240A ALA* 3.0 16.7 + - - +
242A LEU* 3.2 43.8 + - + +
243A PRO 3.8 17.9 - - - +
244A CYS* 4.5 3.1 - - - -
370A ILE* 3.7 37.7 - - + -
378A VAL* 5.5 0.2 - - + -
392A LEU* 4.7 8.7 - - + -
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR 3.0 15.9 + - - -
235A ALA* 3.3 11.1 + - - -
237A VAL* 1.3 76.2 - - - +
239A ARG* 1.3 62.3 + - - +
241A GLY* 3.0 15.6 + - - -
242A LEU 3.9 9.9 + - - +
244A CYS* 3.4 9.4 - - - -
530A LEU* 4.3 13.7 - - + -
534A GLN* 3.2 23.8 + - - +
586A TYR* 5.5 0.2 - - - -
587A VAL* 3.7 49.7 + - + +
589A VAL* 4.6 2.3 - - + +
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Residues in contact with ARG 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178A ALA 5.6 0.6 + - - -
179A LEU* 3.1 21.3 + - - +
180A ASP* 2.7 34.0 + - - +
235A ALA* 2.8 19.0 + - - +
236A MET* 3.3 18.7 + - - +
238A THR* 1.3 74.2 - - - +
240A ALA* 1.3 59.9 + - - +
241A GLY 3.2 1.2 + - - -
452A ASN* 6.4 0.2 - - - -
526A GLN* 4.8 11.1 + - - +
527A ASN* 2.9 34.6 + - - +
530A LEU* 3.8 19.3 - - + +
589A VAL* 3.8 33.3 - - + +
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Residues in contact with ALA 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A LEU* 4.3 9.0 - - + -
183A MET* 4.0 30.8 - - + +
236A MET 3.0 12.2 + - - +
237A VAL 3.0 12.0 + - - +
239A ARG* 1.3 77.1 - - - +
241A GLY* 1.3 58.1 + - - +
242A LEU* 3.7 19.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il